Starting phenix.real_space_refine on Mon Jul 28 04:27:53 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7bty_30191/07_2025/7bty_30191.cif Found real_map, /net/cci-nas-00/data/ceres_data/7bty_30191/07_2025/7bty_30191.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7bty_30191/07_2025/7bty_30191.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7bty_30191/07_2025/7bty_30191.map" model { file = "/net/cci-nas-00/data/ceres_data/7bty_30191/07_2025/7bty_30191.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7bty_30191/07_2025/7bty_30191.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.018 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 44 5.16 5 C 6512 2.51 5 N 1724 2.21 5 O 1888 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 77 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 10168 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 2775 Number of conformers: 1 Conformer: "" Number of residues, atoms: 348, 2775 Classifications: {'peptide': 348} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 12, 'TRANS': 335} Chain breaks: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 2399 Number of conformers: 1 Conformer: "" Number of residues, atoms: 299, 2399 Classifications: {'peptide': 299} Link IDs: {'PTRANS': 8, 'TRANS': 290} Chain breaks: 2 Chain: "C" Number of atoms: 2439 Number of conformers: 1 Conformer: "" Number of residues, atoms: 307, 2439 Classifications: {'peptide': 307} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 6, 'TRANS': 300} Chain breaks: 2 Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 35 Unresolved non-hydrogen dihedrals: 25 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 16 Chain: "L" Number of atoms: 2555 Number of conformers: 1 Conformer: "" Number of residues, atoms: 314, 2555 Classifications: {'peptide': 314} Modifications used: {'COO': 1} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 1} Link IDs: {'PTRANS': 9, 'TRANS': 304} Chain breaks: 4 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Time building chain proxies: 6.24, per 1000 atoms: 0.61 Number of scatterers: 10168 At special positions: 0 Unit cell: (100.845, 104.58, 108.315, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 44 16.00 O 1888 8.00 N 1724 7.00 C 6512 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.17 Conformation dependent library (CDL) restraints added in 1.2 seconds 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2400 Finding SS restraints... Secondary structure from input PDB file: 39 helices and 12 sheets defined 32.3% alpha, 25.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.04 Creating SS restraints... Processing helix chain 'A' and resid 197 through 202 removed outlier: 3.586A pdb=" N LYS A 201 " --> pdb=" O TRP A 197 " (cutoff:3.500A) Processing helix chain 'A' and resid 263 through 270 removed outlier: 3.512A pdb=" N ALA A 270 " --> pdb=" O MET A 266 " (cutoff:3.500A) Processing helix chain 'A' and resid 427 through 435 removed outlier: 3.978A pdb=" N ILE A 431 " --> pdb=" O LEU A 427 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N GLY A 432 " --> pdb=" O GLY A 428 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N GLN A 433 " --> pdb=" O ASN A 429 " (cutoff:3.500A) Processing helix chain 'B' and resid 33 through 40 removed outlier: 3.510A pdb=" N GLN B 38 " --> pdb=" O ALA B 34 " (cutoff:3.500A) Processing helix chain 'B' and resid 80 through 94 Processing helix chain 'B' and resid 119 through 123 removed outlier: 3.546A pdb=" N ASN B 123 " --> pdb=" O ARG B 120 " (cutoff:3.500A) Processing helix chain 'B' and resid 142 through 152 Processing helix chain 'B' and resid 158 through 168 Processing helix chain 'B' and resid 169 through 181 Processing helix chain 'B' and resid 184 through 192 removed outlier: 3.817A pdb=" N MET B 189 " --> pdb=" O ASP B 185 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N LEU B 191 " --> pdb=" O GLN B 187 " (cutoff:3.500A) Processing helix chain 'B' and resid 203 through 216 removed outlier: 3.621A pdb=" N GLU B 208 " --> pdb=" O PRO B 204 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N GLN B 213 " --> pdb=" O ASN B 209 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N LYS B 214 " --> pdb=" O SER B 210 " (cutoff:3.500A) Processing helix chain 'B' and resid 217 through 225 removed outlier: 3.621A pdb=" N SER B 223 " --> pdb=" O SER B 219 " (cutoff:3.500A) Processing helix chain 'B' and resid 229 through 234 Processing helix chain 'B' and resid 234 through 240 Processing helix chain 'B' and resid 247 through 272 removed outlier: 3.702A pdb=" N GLN B 256 " --> pdb=" O VAL B 252 " (cutoff:3.500A) Processing helix chain 'B' and resid 273 through 275 No H-bonds generated for 'chain 'B' and resid 273 through 275' Processing helix chain 'B' and resid 285 through 297 removed outlier: 3.631A pdb=" N CYS B 295 " --> pdb=" O SER B 291 " (cutoff:3.500A) Processing helix chain 'B' and resid 304 through 312 Processing helix chain 'B' and resid 313 through 325 removed outlier: 3.540A pdb=" N GLN B 318 " --> pdb=" O LYS B 314 " (cutoff:3.500A) Processing helix chain 'C' and resid 19 through 31 removed outlier: 3.559A pdb=" N ILE C 23 " --> pdb=" O SER C 19 " (cutoff:3.500A) Processing helix chain 'C' and resid 34 through 40 removed outlier: 3.711A pdb=" N SER C 39 " --> pdb=" O GLU C 35 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N MET C 40 " --> pdb=" O GLU C 36 " (cutoff:3.500A) Processing helix chain 'C' and resid 51 through 55 removed outlier: 3.780A pdb=" N LEU C 54 " --> pdb=" O ASN C 51 " (cutoff:3.500A) Processing helix chain 'C' and resid 73 through 84 Processing helix chain 'C' and resid 104 through 106 No H-bonds generated for 'chain 'C' and resid 104 through 106' Processing helix chain 'C' and resid 107 through 121 Processing helix chain 'C' and resid 122 through 132 removed outlier: 3.597A pdb=" N PHE C 131 " --> pdb=" O ASP C 127 " (cutoff:3.500A) Processing helix chain 'C' and resid 133 through 140 removed outlier: 3.591A pdb=" N ASN C 138 " --> pdb=" O THR C 134 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N GLU C 139 " --> pdb=" O LYS C 135 " (cutoff:3.500A) Processing helix chain 'C' and resid 156 through 169 Processing helix chain 'C' and resid 203 through 206 removed outlier: 3.649A pdb=" N HIS C 206 " --> pdb=" O LYS C 203 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 203 through 206' Processing helix chain 'C' and resid 207 through 227 removed outlier: 3.788A pdb=" N LYS C 213 " --> pdb=" O LYS C 209 " (cutoff:3.500A) removed outlier: 4.488A pdb=" N LEU C 216 " --> pdb=" O GLY C 212 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N GLN C 217 " --> pdb=" O LYS C 213 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N VAL C 219 " --> pdb=" O GLU C 215 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N LYS C 220 " --> pdb=" O LEU C 216 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N GLN C 224 " --> pdb=" O LYS C 220 " (cutoff:3.500A) Processing helix chain 'C' and resid 227 through 241 removed outlier: 3.583A pdb=" N SER C 234 " --> pdb=" O GLN C 230 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N LYS C 241 " --> pdb=" O LEU C 237 " (cutoff:3.500A) Processing helix chain 'C' and resid 251 through 265 removed outlier: 3.766A pdb=" N VAL C 261 " --> pdb=" O ALA C 257 " (cutoff:3.500A) Processing helix chain 'C' and resid 267 through 280 removed outlier: 4.018A pdb=" N ILE C 271 " --> pdb=" O ASP C 267 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N GLU C 276 " --> pdb=" O ARG C 272 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N THR C 278 " --> pdb=" O LYS C 274 " (cutoff:3.500A) Processing helix chain 'C' and resid 280 through 296 removed outlier: 3.927A pdb=" N LEU C 284 " --> pdb=" O GLY C 280 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N SER C 286 " --> pdb=" O GLU C 282 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N HIS C 296 " --> pdb=" O ASP C 292 " (cutoff:3.500A) Processing helix chain 'C' and resid 316 through 324 removed outlier: 3.576A pdb=" N TYR C 320 " --> pdb=" O VAL C 316 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N LEU C 322 " --> pdb=" O SER C 318 " (cutoff:3.500A) Processing helix chain 'L' and resid 4 through 17 removed outlier: 4.122A pdb=" N ARG L 10 " --> pdb=" O ASP L 6 " (cutoff:3.500A) Processing helix chain 'L' and resid 19 through 23 Processing helix chain 'L' and resid 29 through 34 Processing helix chain 'L' and resid 81 through 87 removed outlier: 4.033A pdb=" N ARG L 86 " --> pdb=" O LYS L 83 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N ASN L 87 " --> pdb=" O PHE L 84 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 126 through 129 removed outlier: 3.603A pdb=" N TYR A 140 " --> pdb=" O GLY A 128 " (cutoff:3.500A) removed outlier: 7.359A pdb=" N ALA A 139 " --> pdb=" O ARG A 164 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N ARG A 164 " --> pdb=" O ALA A 139 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ASN A 175 " --> pdb=" O ASN A 159 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N GLY A 165 " --> pdb=" O HIS A 169 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N HIS A 169 " --> pdb=" O GLY A 165 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N SER A 170 " --> pdb=" O PHE A 194 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N PHE A 194 " --> pdb=" O SER A 170 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N SER A 184 " --> pdb=" O LEU A 180 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N GLY A 416 " --> pdb=" O TYR A 390 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 464 through 466 removed outlier: 7.305A pdb=" N ALA A 465 " --> pdb=" O TYR B 23 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'B' and resid 41 through 42 Processing sheet with id=AA4, first strand: chain 'B' and resid 67 through 69 Processing sheet with id=AA5, first strand: chain 'C' and resid 5 through 7 removed outlier: 4.459A pdb=" N THR C 69 " --> pdb=" O LEU C 65 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 46 through 47 removed outlier: 6.683A pdb=" N ILE C 46 " --> pdb=" O ARG C 305 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'L' and resid 44 through 52 removed outlier: 3.624A pdb=" N ASN L 57 " --> pdb=" O ASN L 49 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N THR L 55 " --> pdb=" O SER L 51 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ASP L 60 " --> pdb=" O ASN L 68 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N LEU L 179 " --> pdb=" O SER L 174 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N GLN L 195 " --> pdb=" O ARG L 188 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'L' and resid 209 through 210 removed outlier: 4.085A pdb=" N VAL L 210 " --> pdb=" O ALA L 235 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N THR L 251 " --> pdb=" O GLY L 234 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N GLU L 236 " --> pdb=" O SER L 249 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N SER L 249 " --> pdb=" O GLU L 236 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'L' and resid 230 through 231 removed outlier: 3.715A pdb=" N TYR L 255 " --> pdb=" O SER L 230 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'L' and resid 282 through 284 Processing sheet with id=AB2, first strand: chain 'L' and resid 413 through 421 removed outlier: 3.764A pdb=" N THR L 413 " --> pdb=" O LYS L 434 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N SER L 421 " --> pdb=" O THR L 426 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N THR L 426 " --> pdb=" O SER L 421 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N GLU L 445 " --> pdb=" O LYS L 484 " (cutoff:3.500A) removed outlier: 4.955A pdb=" N LYS L 484 " --> pdb=" O GLU L 445 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N VAL L 447 " --> pdb=" O PRO L 482 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'L' and resid 413 through 421 removed outlier: 3.764A pdb=" N THR L 413 " --> pdb=" O LYS L 434 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N SER L 421 " --> pdb=" O THR L 426 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N THR L 426 " --> pdb=" O SER L 421 " (cutoff:3.500A) 458 hydrogen bonds defined for protein. 1287 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.20 Time building geometry restraints manager: 2.69 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.98 - 1.15: 2 1.15 - 1.32: 1686 1.32 - 1.49: 4442 1.49 - 1.66: 4191 1.66 - 1.83: 65 Bond restraints: 10386 Sorted by residual: bond pdb=" C GLN A 433 " pdb=" O GLN A 433 " ideal model delta sigma weight residual 1.233 0.979 0.254 1.46e-02 4.69e+03 3.03e+02 bond pdb=" CA GLN A 433 " pdb=" C GLN A 433 " ideal model delta sigma weight residual 1.520 1.322 0.197 1.40e-02 5.10e+03 1.99e+02 bond pdb=" CA GLN A 433 " pdb=" CB GLN A 433 " ideal model delta sigma weight residual 1.537 1.402 0.134 1.67e-02 3.59e+03 6.46e+01 bond pdb=" C GLN A 433 " pdb=" N LEU A 434 " ideal model delta sigma weight residual 1.333 1.232 0.101 1.49e-02 4.50e+03 4.57e+01 bond pdb=" CD GLN A 433 " pdb=" NE2 GLN A 433 " ideal model delta sigma weight residual 1.328 1.186 0.142 2.10e-02 2.27e+03 4.56e+01 ... (remaining 10381 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.54: 13797 3.54 - 7.08: 197 7.08 - 10.62: 34 10.62 - 14.16: 5 14.16 - 17.70: 1 Bond angle restraints: 14034 Sorted by residual: angle pdb=" C ALA B 127 " pdb=" N LEU B 128 " pdb=" CA LEU B 128 " ideal model delta sigma weight residual 122.37 113.15 9.22 9.30e-01 1.16e+00 9.84e+01 angle pdb=" N GLU C 98 " pdb=" CA GLU C 98 " pdb=" C GLU C 98 " ideal model delta sigma weight residual 110.80 128.50 -17.70 2.13e+00 2.20e-01 6.90e+01 angle pdb=" C THR C 87 " pdb=" N SER C 88 " pdb=" CA SER C 88 " ideal model delta sigma weight residual 121.70 135.52 -13.82 1.80e+00 3.09e-01 5.90e+01 angle pdb=" C TYR L 147 " pdb=" N TYR L 148 " pdb=" CA TYR L 148 " ideal model delta sigma weight residual 123.21 114.20 9.01 1.19e+00 7.06e-01 5.74e+01 angle pdb=" CA THR C 87 " pdb=" C THR C 87 " pdb=" N SER C 88 " ideal model delta sigma weight residual 116.84 104.59 12.25 1.71e+00 3.42e-01 5.13e+01 ... (remaining 14029 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.20: 5332 17.20 - 34.39: 682 34.39 - 51.59: 147 51.59 - 68.79: 13 68.79 - 85.98: 12 Dihedral angle restraints: 6186 sinusoidal: 2480 harmonic: 3706 Sorted by residual: dihedral pdb=" CA LEU B 128 " pdb=" C LEU B 128 " pdb=" N PRO B 129 " pdb=" CA PRO B 129 " ideal model delta harmonic sigma weight residual 180.00 115.98 64.02 0 5.00e+00 4.00e-02 1.64e+02 dihedral pdb=" N GLU C 98 " pdb=" C GLU C 98 " pdb=" CA GLU C 98 " pdb=" CB GLU C 98 " ideal model delta harmonic sigma weight residual 122.80 150.43 -27.63 0 2.50e+00 1.60e-01 1.22e+02 dihedral pdb=" C GLU C 98 " pdb=" N GLU C 98 " pdb=" CA GLU C 98 " pdb=" CB GLU C 98 " ideal model delta harmonic sigma weight residual -122.60 -149.54 26.94 0 2.50e+00 1.60e-01 1.16e+02 ... (remaining 6183 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.265: 1570 0.265 - 0.529: 2 0.529 - 0.794: 0 0.794 - 1.058: 0 1.058 - 1.323: 1 Chirality restraints: 1573 Sorted by residual: chirality pdb=" CA GLU C 98 " pdb=" N GLU C 98 " pdb=" C GLU C 98 " pdb=" CB GLU C 98 " both_signs ideal model delta sigma weight residual False 2.51 1.19 1.32 2.00e-01 2.50e+01 4.37e+01 chirality pdb=" CA GLN A 433 " pdb=" N GLN A 433 " pdb=" C GLN A 433 " pdb=" CB GLN A 433 " both_signs ideal model delta sigma weight residual False 2.51 2.18 0.33 2.00e-01 2.50e+01 2.65e+00 chirality pdb=" CA GLU C 97 " pdb=" N GLU C 97 " pdb=" C GLU C 97 " pdb=" CB GLU C 97 " both_signs ideal model delta sigma weight residual False 2.51 2.23 0.29 2.00e-01 2.50e+01 2.03e+00 ... (remaining 1570 not shown) Planarity restraints: 1764 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA THR C 87 " 0.046 2.00e-02 2.50e+03 1.00e-01 1.01e+02 pdb=" C THR C 87 " -0.173 2.00e-02 2.50e+03 pdb=" O THR C 87 " 0.071 2.00e-02 2.50e+03 pdb=" N SER C 88 " 0.056 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU C 60 " 0.093 5.00e-02 4.00e+02 1.39e-01 3.07e+01 pdb=" N PRO C 61 " -0.240 5.00e-02 4.00e+02 pdb=" CA PRO C 61 " 0.075 5.00e-02 4.00e+02 pdb=" CD PRO C 61 " 0.072 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLY A 432 " 0.024 2.00e-02 2.50e+03 4.83e-02 2.33e+01 pdb=" C GLY A 432 " -0.083 2.00e-02 2.50e+03 pdb=" O GLY A 432 " 0.031 2.00e-02 2.50e+03 pdb=" N GLN A 433 " 0.029 2.00e-02 2.50e+03 ... (remaining 1761 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 2304 2.78 - 3.31: 8310 3.31 - 3.84: 16242 3.84 - 4.37: 20023 4.37 - 4.90: 35344 Nonbonded interactions: 82223 Sorted by model distance: nonbonded pdb=" O GLN C 230 " pdb=" OG SER C 234 " model vdw 2.247 3.040 nonbonded pdb=" OG SER B 184 " pdb=" OE2 GLU B 301 " model vdw 2.254 3.040 nonbonded pdb=" O THR B 165 " pdb=" OG1 THR B 169 " model vdw 2.266 3.040 nonbonded pdb=" OG1 THR A 265 " pdb=" OD2 ASP A 377 " model vdw 2.279 3.040 nonbonded pdb=" OG SER A 344 " pdb=" O SER A 348 " model vdw 2.279 3.040 ... (remaining 82218 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.570 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.440 Check model and map are aligned: 0.080 Set scattering table: 0.120 Process input model: 25.600 Find NCS groups from input model: 0.220 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.940 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.020 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7655 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.254 10386 Z= 0.498 Angle : 1.151 17.699 14034 Z= 0.638 Chirality : 0.069 1.323 1573 Planarity : 0.009 0.139 1764 Dihedral : 15.857 85.983 3786 Min Nonbonded Distance : 2.247 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.64 % Allowed : 10.23 % Favored : 89.13 % Rotamer: Outliers : 0.70 % Allowed : 11.89 % Favored : 87.40 % Cbeta Deviations : 0.17 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 8.57 % Twisted General : 0.66 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.57 (0.18), residues: 1242 helix: -4.33 (0.13), residues: 362 sheet: -3.05 (0.22), residues: 396 loop : -3.44 (0.22), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP A 323 HIS 0.012 0.002 HIS A 310 PHE 0.038 0.003 PHE B 68 TYR 0.029 0.003 TYR A 140 ARG 0.010 0.001 ARG B 120 Details of bonding type rmsd hydrogen bonds : bond 0.27295 ( 443) hydrogen bonds : angle 10.57915 ( 1287) covalent geometry : bond 0.01049 (10386) covalent geometry : angle 1.15100 (14034) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 1149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 156 time to evaluate : 1.057 Fit side-chains REVERT: A 300 LYS cc_start: 0.8372 (tttt) cc_final: 0.8104 (tttm) REVERT: A 385 ASP cc_start: 0.8050 (m-30) cc_final: 0.7394 (m-30) REVERT: B 136 LYS cc_start: 0.8181 (mttp) cc_final: 0.7906 (mmtt) REVERT: B 189 MET cc_start: 0.9165 (mmm) cc_final: 0.8276 (mmt) REVERT: B 236 GLU cc_start: 0.8080 (mm-30) cc_final: 0.7442 (pm20) REVERT: C 11 LYS cc_start: 0.7420 (ptmt) cc_final: 0.7157 (ptmt) REVERT: C 40 MET cc_start: 0.9016 (ptt) cc_final: 0.8773 (ptm) REVERT: C 102 ILE cc_start: 0.8568 (mm) cc_final: 0.8175 (mm) REVERT: C 111 GLU cc_start: 0.8116 (tm-30) cc_final: 0.7903 (tp30) REVERT: C 121 GLU cc_start: 0.7505 (mm-30) cc_final: 0.7115 (mm-30) REVERT: C 150 TYR cc_start: 0.8141 (m-80) cc_final: 0.7840 (m-80) REVERT: C 317 MET cc_start: 0.8282 (tpp) cc_final: 0.7934 (tpp) REVERT: L 5 MET cc_start: 0.6691 (ttp) cc_final: 0.6314 (ttp) REVERT: L 146 MET cc_start: 0.8010 (ptp) cc_final: 0.7545 (ptm) REVERT: L 168 MET cc_start: 0.7353 (mtp) cc_final: 0.7125 (mtp) REVERT: L 254 TYR cc_start: 0.7447 (t80) cc_final: 0.6703 (t80) outliers start: 8 outliers final: 3 residues processed: 163 average time/residue: 0.2677 time to fit residues: 58.4647 Evaluate side-chains 122 residues out of total 1149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 119 time to evaluate : 1.189 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 274 ASP Chi-restraints excluded: chain C residue 97 GLU Chi-restraints excluded: chain C residue 98 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 104 optimal weight: 4.9990 chunk 93 optimal weight: 0.7980 chunk 52 optimal weight: 0.9980 chunk 32 optimal weight: 1.9990 chunk 63 optimal weight: 2.9990 chunk 50 optimal weight: 1.9990 chunk 97 optimal weight: 1.9990 chunk 37 optimal weight: 4.9990 chunk 59 optimal weight: 0.5980 chunk 72 optimal weight: 4.9990 chunk 112 optimal weight: 6.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 196 ASN A 207 GLN A 269 GLN A 273 GLN A 280 HIS A 303 ASN A 310 HIS A 369 GLN A 411 HIS ** A 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 466 HIS B 87 GLN B 94 ASN B 101 HIS B 178 GLN B 321 GLN C 7 HIS C 129 GLN C 133 ASN C 224 GLN C 227 ASN C 285 ASN L 57 ASN L 195 GLN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.171685 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.122461 restraints weight = 10636.908| |-----------------------------------------------------------------------------| r_work (start): 0.3272 rms_B_bonded: 1.79 r_work: 0.3111 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.2961 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.2961 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7932 moved from start: 0.1727 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 10386 Z= 0.165 Angle : 0.694 9.451 14034 Z= 0.366 Chirality : 0.044 0.219 1573 Planarity : 0.006 0.103 1764 Dihedral : 7.579 68.594 1366 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.24 % Allowed : 8.29 % Favored : 91.47 % Rotamer: Outliers : 1.76 % Allowed : 14.71 % Favored : 83.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 8.57 % Twisted General : 0.25 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.01 (0.21), residues: 1242 helix: -2.26 (0.22), residues: 369 sheet: -2.37 (0.24), residues: 383 loop : -3.03 (0.24), residues: 490 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 323 HIS 0.004 0.001 HIS A 310 PHE 0.021 0.002 PHE B 68 TYR 0.017 0.002 TYR C 260 ARG 0.004 0.000 ARG A 366 Details of bonding type rmsd hydrogen bonds : bond 0.04080 ( 443) hydrogen bonds : angle 5.64858 ( 1287) covalent geometry : bond 0.00368 (10386) covalent geometry : angle 0.69393 (14034) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 1149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 140 time to evaluate : 1.112 Fit side-chains REVERT: A 157 ARG cc_start: 0.8111 (ptt90) cc_final: 0.7858 (ptt-90) REVERT: A 161 GLU cc_start: 0.8554 (tt0) cc_final: 0.7539 (mt-10) REVERT: A 266 MET cc_start: 0.9325 (mmt) cc_final: 0.9083 (mmm) REVERT: A 291 MET cc_start: 0.7771 (mmm) cc_final: 0.7463 (tpp) REVERT: A 300 LYS cc_start: 0.8685 (tttt) cc_final: 0.8471 (tttm) REVERT: B 135 TYR cc_start: 0.8348 (t80) cc_final: 0.8129 (t80) REVERT: B 136 LYS cc_start: 0.8351 (mttp) cc_final: 0.7973 (mmtt) REVERT: B 168 ASP cc_start: 0.8861 (m-30) cc_final: 0.8610 (m-30) REVERT: B 189 MET cc_start: 0.9187 (mmm) cc_final: 0.8502 (mmt) REVERT: B 190 GLU cc_start: 0.8883 (tt0) cc_final: 0.8676 (tt0) REVERT: C 102 ILE cc_start: 0.7880 (mm) cc_final: 0.7636 (mm) REVERT: C 260 TYR cc_start: 0.8214 (t80) cc_final: 0.7856 (t80) REVERT: C 317 MET cc_start: 0.8058 (tpp) cc_final: 0.7749 (tpp) REVERT: L 38 ARG cc_start: 0.7488 (ttp-170) cc_final: 0.7151 (ttp-170) REVERT: L 146 MET cc_start: 0.8448 (ptp) cc_final: 0.8242 (ptm) REVERT: L 166 GLN cc_start: 0.8781 (mt0) cc_final: 0.8186 (tt0) REVERT: L 168 MET cc_start: 0.8192 (mtp) cc_final: 0.7880 (mtp) REVERT: L 253 ARG cc_start: 0.7890 (ptt-90) cc_final: 0.7605 (ptt-90) outliers start: 20 outliers final: 12 residues processed: 152 average time/residue: 0.2412 time to fit residues: 50.9083 Evaluate side-chains 132 residues out of total 1149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 120 time to evaluate : 1.069 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 197 TRP Chi-restraints excluded: chain A residue 213 SER Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 359 SER Chi-restraints excluded: chain B residue 45 THR Chi-restraints excluded: chain B residue 110 THR Chi-restraints excluded: chain B residue 144 VAL Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain C residue 97 GLU Chi-restraints excluded: chain C residue 134 THR Chi-restraints excluded: chain C residue 247 VAL Chi-restraints excluded: chain L residue 139 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 92 optimal weight: 6.9990 chunk 89 optimal weight: 8.9990 chunk 72 optimal weight: 2.9990 chunk 78 optimal weight: 4.9990 chunk 18 optimal weight: 8.9990 chunk 77 optimal weight: 5.9990 chunk 90 optimal weight: 7.9990 chunk 7 optimal weight: 0.7980 chunk 0 optimal weight: 7.9990 chunk 88 optimal weight: 1.9990 chunk 104 optimal weight: 4.9990 overall best weight: 3.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 303 ASN ** A 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 112 ASN B 318 GLN C 50 ASN C 133 ASN C 258 ASN C 262 GLN L 68 ASN L 212 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.167966 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 83)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.117985 restraints weight = 10860.517| |-----------------------------------------------------------------------------| r_work (start): 0.3206 rms_B_bonded: 1.88 r_work: 0.3038 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.3038 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7890 moved from start: 0.1952 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.054 10386 Z= 0.307 Angle : 0.785 7.622 14034 Z= 0.407 Chirality : 0.048 0.182 1573 Planarity : 0.007 0.124 1764 Dihedral : 7.377 64.648 1361 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 8.44 Ramachandran Plot: Outliers : 0.32 % Allowed : 9.98 % Favored : 89.69 % Rotamer: Outliers : 3.08 % Allowed : 16.56 % Favored : 80.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 8.57 % Twisted General : 0.33 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.40 (0.22), residues: 1242 helix: -1.10 (0.26), residues: 353 sheet: -2.30 (0.25), residues: 397 loop : -2.95 (0.25), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 323 HIS 0.005 0.001 HIS A 422 PHE 0.026 0.002 PHE B 18 TYR 0.024 0.002 TYR A 140 ARG 0.006 0.001 ARG A 208 Details of bonding type rmsd hydrogen bonds : bond 0.04358 ( 443) hydrogen bonds : angle 5.40306 ( 1287) covalent geometry : bond 0.00726 (10386) covalent geometry : angle 0.78519 (14034) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 1149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 125 time to evaluate : 1.132 Fit side-chains REVERT: A 157 ARG cc_start: 0.7948 (ptt90) cc_final: 0.7566 (ptt180) REVERT: A 266 MET cc_start: 0.9174 (mmt) cc_final: 0.8922 (mmm) REVERT: A 300 LYS cc_start: 0.8539 (tttt) cc_final: 0.8300 (tttm) REVERT: A 385 ASP cc_start: 0.8453 (m-30) cc_final: 0.7923 (m-30) REVERT: A 390 TYR cc_start: 0.8900 (p90) cc_final: 0.8552 (p90) REVERT: A 446 LEU cc_start: 0.9122 (OUTLIER) cc_final: 0.8859 (tt) REVERT: B 136 LYS cc_start: 0.8316 (mttp) cc_final: 0.7949 (mmtt) REVERT: B 189 MET cc_start: 0.9183 (mmm) cc_final: 0.8498 (mmt) REVERT: B 190 GLU cc_start: 0.8749 (tt0) cc_final: 0.8506 (tt0) REVERT: B 236 GLU cc_start: 0.8401 (mm-30) cc_final: 0.7703 (pm20) REVERT: C 40 MET cc_start: 0.8937 (ptt) cc_final: 0.8684 (ptm) REVERT: C 102 ILE cc_start: 0.8102 (mm) cc_final: 0.7800 (mm) REVERT: C 119 ASP cc_start: 0.8117 (t0) cc_final: 0.7848 (t0) REVERT: C 317 MET cc_start: 0.8067 (tpp) cc_final: 0.7808 (tpp) REVERT: L 13 TYR cc_start: 0.6630 (m-10) cc_final: 0.5955 (m-80) REVERT: L 146 MET cc_start: 0.8418 (ptp) cc_final: 0.8171 (ptm) REVERT: L 168 MET cc_start: 0.7998 (mtp) cc_final: 0.7615 (mtp) REVERT: L 253 ARG cc_start: 0.7853 (ptt-90) cc_final: 0.7552 (ptt-90) REVERT: L 254 TYR cc_start: 0.7434 (t80) cc_final: 0.7015 (t80) outliers start: 35 outliers final: 25 residues processed: 154 average time/residue: 0.2377 time to fit residues: 51.6330 Evaluate side-chains 143 residues out of total 1149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 117 time to evaluate : 1.088 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 181 SER Chi-restraints excluded: chain A residue 197 TRP Chi-restraints excluded: chain A residue 213 SER Chi-restraints excluded: chain A residue 359 SER Chi-restraints excluded: chain A residue 420 VAL Chi-restraints excluded: chain A residue 444 ILE Chi-restraints excluded: chain A residue 446 LEU Chi-restraints excluded: chain A residue 481 LEU Chi-restraints excluded: chain B residue 22 THR Chi-restraints excluded: chain B residue 43 THR Chi-restraints excluded: chain B residue 45 THR Chi-restraints excluded: chain B residue 110 THR Chi-restraints excluded: chain B residue 120 ARG Chi-restraints excluded: chain B residue 123 ASN Chi-restraints excluded: chain B residue 144 VAL Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 252 VAL Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 97 GLU Chi-restraints excluded: chain C residue 134 THR Chi-restraints excluded: chain C residue 219 VAL Chi-restraints excluded: chain C residue 247 VAL Chi-restraints excluded: chain C residue 277 GLN Chi-restraints excluded: chain L residue 5 MET Chi-restraints excluded: chain L residue 139 LYS Chi-restraints excluded: chain L residue 204 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 85 optimal weight: 6.9990 chunk 32 optimal weight: 4.9990 chunk 46 optimal weight: 1.9990 chunk 65 optimal weight: 0.9990 chunk 77 optimal weight: 2.9990 chunk 0 optimal weight: 6.9990 chunk 28 optimal weight: 2.9990 chunk 81 optimal weight: 10.0000 chunk 94 optimal weight: 2.9990 chunk 117 optimal weight: 8.9990 chunk 99 optimal weight: 5.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 424 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 256 GLN C 133 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.169840 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.121331 restraints weight = 10750.593| |-----------------------------------------------------------------------------| r_work (start): 0.3234 rms_B_bonded: 2.00 r_work: 0.3047 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3047 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7863 moved from start: 0.2191 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.044 10386 Z= 0.242 Angle : 0.716 7.956 14034 Z= 0.373 Chirality : 0.046 0.165 1573 Planarity : 0.006 0.107 1764 Dihedral : 7.118 68.555 1361 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 8.29 Ramachandran Plot: Outliers : 0.24 % Allowed : 9.42 % Favored : 90.34 % Rotamer: Outliers : 4.05 % Allowed : 16.48 % Favored : 79.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 8.57 % Twisted General : 0.25 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.08 (0.23), residues: 1242 helix: -0.69 (0.27), residues: 362 sheet: -2.07 (0.26), residues: 386 loop : -2.96 (0.25), residues: 494 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 323 HIS 0.004 0.001 HIS A 310 PHE 0.023 0.002 PHE B 18 TYR 0.020 0.002 TYR B 164 ARG 0.006 0.000 ARG B 120 Details of bonding type rmsd hydrogen bonds : bond 0.03764 ( 443) hydrogen bonds : angle 5.13753 ( 1287) covalent geometry : bond 0.00566 (10386) covalent geometry : angle 0.71584 (14034) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 1149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 121 time to evaluate : 1.051 Fit side-chains REVERT: A 157 ARG cc_start: 0.7944 (ptt90) cc_final: 0.7602 (ptt180) REVERT: A 266 MET cc_start: 0.9184 (mmt) cc_final: 0.8939 (mmm) REVERT: A 291 MET cc_start: 0.7479 (mmm) cc_final: 0.7239 (tpp) REVERT: A 300 LYS cc_start: 0.8571 (tttt) cc_final: 0.8333 (tttm) REVERT: A 385 ASP cc_start: 0.8373 (m-30) cc_final: 0.7799 (m-30) REVERT: A 390 TYR cc_start: 0.8852 (p90) cc_final: 0.8529 (p90) REVERT: A 446 LEU cc_start: 0.9012 (OUTLIER) cc_final: 0.8791 (tt) REVERT: B 135 TYR cc_start: 0.8530 (t80) cc_final: 0.8302 (t80) REVERT: B 136 LYS cc_start: 0.8348 (mttp) cc_final: 0.7981 (mmtt) REVERT: B 189 MET cc_start: 0.9196 (mmm) cc_final: 0.8459 (mmt) REVERT: B 190 GLU cc_start: 0.8747 (tt0) cc_final: 0.8520 (tt0) REVERT: C 11 LYS cc_start: 0.7418 (ptmt) cc_final: 0.7020 (ptmt) REVERT: C 40 MET cc_start: 0.8945 (ptt) cc_final: 0.8711 (ptm) REVERT: C 66 ASP cc_start: 0.4745 (p0) cc_final: 0.4542 (p0) REVERT: C 102 ILE cc_start: 0.8007 (mm) cc_final: 0.7735 (mm) REVERT: C 111 GLU cc_start: 0.8293 (OUTLIER) cc_final: 0.7829 (tm-30) REVERT: C 119 ASP cc_start: 0.8049 (t0) cc_final: 0.7717 (t0) REVERT: C 303 GLU cc_start: 0.7564 (OUTLIER) cc_final: 0.7249 (pt0) REVERT: C 317 MET cc_start: 0.8143 (tpp) cc_final: 0.7836 (tpp) REVERT: L 13 TYR cc_start: 0.6502 (m-10) cc_final: 0.5959 (m-80) REVERT: L 38 ARG cc_start: 0.7400 (ttp-170) cc_final: 0.7132 (ttp-170) REVERT: L 85 MET cc_start: 0.2105 (mmp) cc_final: 0.1468 (mtp) REVERT: L 146 MET cc_start: 0.8459 (ptp) cc_final: 0.8216 (ptm) REVERT: L 148 TYR cc_start: 0.8226 (OUTLIER) cc_final: 0.7816 (p90) REVERT: L 253 ARG cc_start: 0.7786 (ptt-90) cc_final: 0.7550 (ptt-90) REVERT: L 254 TYR cc_start: 0.7521 (t80) cc_final: 0.7056 (t80) outliers start: 46 outliers final: 31 residues processed: 155 average time/residue: 0.2256 time to fit residues: 49.0846 Evaluate side-chains 149 residues out of total 1149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 114 time to evaluate : 1.173 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 181 SER Chi-restraints excluded: chain A residue 197 TRP Chi-restraints excluded: chain A residue 213 SER Chi-restraints excluded: chain A residue 248 SER Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 359 SER Chi-restraints excluded: chain A residue 396 SER Chi-restraints excluded: chain A residue 420 VAL Chi-restraints excluded: chain A residue 440 THR Chi-restraints excluded: chain A residue 446 LEU Chi-restraints excluded: chain A residue 481 LEU Chi-restraints excluded: chain B residue 22 THR Chi-restraints excluded: chain B residue 43 THR Chi-restraints excluded: chain B residue 45 THR Chi-restraints excluded: chain B residue 110 THR Chi-restraints excluded: chain B residue 120 ARG Chi-restraints excluded: chain B residue 123 ASN Chi-restraints excluded: chain B residue 144 VAL Chi-restraints excluded: chain B residue 203 THR Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 252 VAL Chi-restraints excluded: chain C residue 41 VAL Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 97 GLU Chi-restraints excluded: chain C residue 111 GLU Chi-restraints excluded: chain C residue 134 THR Chi-restraints excluded: chain C residue 219 VAL Chi-restraints excluded: chain C residue 247 VAL Chi-restraints excluded: chain C residue 284 LEU Chi-restraints excluded: chain C residue 303 GLU Chi-restraints excluded: chain L residue 5 MET Chi-restraints excluded: chain L residue 139 LYS Chi-restraints excluded: chain L residue 148 TYR Chi-restraints excluded: chain L residue 204 LEU Chi-restraints excluded: chain L residue 304 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 28 optimal weight: 4.9990 chunk 121 optimal weight: 7.9990 chunk 98 optimal weight: 5.9990 chunk 9 optimal weight: 5.9990 chunk 16 optimal weight: 4.9990 chunk 52 optimal weight: 0.9980 chunk 123 optimal weight: 0.5980 chunk 41 optimal weight: 0.9980 chunk 2 optimal weight: 6.9990 chunk 10 optimal weight: 1.9990 chunk 37 optimal weight: 5.9990 overall best weight: 1.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 GLN ** A 424 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 318 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3853 r_free = 0.3853 target = 0.169962 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.124039 restraints weight = 10679.329| |-----------------------------------------------------------------------------| r_work (start): 0.3294 rms_B_bonded: 1.87 r_work: 0.3093 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.2946 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.2946 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7944 moved from start: 0.2338 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 10386 Z= 0.203 Angle : 0.682 7.491 14034 Z= 0.354 Chirality : 0.044 0.159 1573 Planarity : 0.006 0.104 1764 Dihedral : 6.932 71.084 1361 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 8.14 Ramachandran Plot: Outliers : 0.24 % Allowed : 9.50 % Favored : 90.26 % Rotamer: Outliers : 4.41 % Allowed : 17.18 % Favored : 78.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 8.57 % Twisted General : 0.16 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.85 (0.23), residues: 1242 helix: -0.37 (0.28), residues: 367 sheet: -1.97 (0.26), residues: 384 loop : -2.93 (0.25), residues: 491 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 323 HIS 0.004 0.001 HIS A 310 PHE 0.020 0.002 PHE B 18 TYR 0.018 0.002 TYR B 164 ARG 0.005 0.000 ARG B 120 Details of bonding type rmsd hydrogen bonds : bond 0.03494 ( 443) hydrogen bonds : angle 4.99651 ( 1287) covalent geometry : bond 0.00474 (10386) covalent geometry : angle 0.68194 (14034) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 1149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 123 time to evaluate : 1.167 Fit side-chains REVERT: A 157 ARG cc_start: 0.7995 (ptt90) cc_final: 0.7693 (ptt-90) REVERT: A 266 MET cc_start: 0.9289 (mmt) cc_final: 0.9069 (mmm) REVERT: A 291 MET cc_start: 0.7764 (mmm) cc_final: 0.7492 (tpp) REVERT: A 385 ASP cc_start: 0.8545 (m-30) cc_final: 0.7968 (m-30) REVERT: A 390 TYR cc_start: 0.8890 (p90) cc_final: 0.8557 (p90) REVERT: B 136 LYS cc_start: 0.8383 (mttp) cc_final: 0.7964 (mmtt) REVERT: B 189 MET cc_start: 0.9215 (mmm) cc_final: 0.8574 (mmt) REVERT: C 40 MET cc_start: 0.8967 (ptt) cc_final: 0.8728 (ptm) REVERT: C 102 ILE cc_start: 0.8012 (mm) cc_final: 0.7723 (mm) REVERT: C 111 GLU cc_start: 0.8380 (OUTLIER) cc_final: 0.7877 (tm-30) REVERT: C 119 ASP cc_start: 0.8266 (t0) cc_final: 0.7989 (t0) REVERT: C 303 GLU cc_start: 0.7738 (OUTLIER) cc_final: 0.7475 (pt0) REVERT: C 317 MET cc_start: 0.8049 (tpp) cc_final: 0.7779 (tpp) REVERT: L 13 TYR cc_start: 0.6449 (m-10) cc_final: 0.5966 (m-80) REVERT: L 38 ARG cc_start: 0.7455 (ttp-170) cc_final: 0.7166 (ttp-170) REVERT: L 49 ASN cc_start: 0.7613 (OUTLIER) cc_final: 0.7181 (m-40) REVERT: L 85 MET cc_start: 0.1489 (mmp) cc_final: 0.0830 (mtp) REVERT: L 146 MET cc_start: 0.8414 (ptp) cc_final: 0.8177 (ptm) REVERT: L 148 TYR cc_start: 0.8235 (OUTLIER) cc_final: 0.7826 (p90) REVERT: L 253 ARG cc_start: 0.7845 (ptt-90) cc_final: 0.7616 (ptt-90) REVERT: L 254 TYR cc_start: 0.7628 (t80) cc_final: 0.7085 (t80) outliers start: 50 outliers final: 34 residues processed: 157 average time/residue: 0.2595 time to fit residues: 57.1999 Evaluate side-chains 156 residues out of total 1149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 118 time to evaluate : 1.098 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 197 TRP Chi-restraints excluded: chain A residue 213 SER Chi-restraints excluded: chain A residue 248 SER Chi-restraints excluded: chain A residue 327 ASP Chi-restraints excluded: chain A residue 359 SER Chi-restraints excluded: chain A residue 396 SER Chi-restraints excluded: chain A residue 420 VAL Chi-restraints excluded: chain A residue 427 LEU Chi-restraints excluded: chain A residue 440 THR Chi-restraints excluded: chain A residue 481 LEU Chi-restraints excluded: chain B residue 22 THR Chi-restraints excluded: chain B residue 43 THR Chi-restraints excluded: chain B residue 45 THR Chi-restraints excluded: chain B residue 110 THR Chi-restraints excluded: chain B residue 120 ARG Chi-restraints excluded: chain B residue 123 ASN Chi-restraints excluded: chain B residue 139 ILE Chi-restraints excluded: chain B residue 144 VAL Chi-restraints excluded: chain B residue 203 THR Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 252 VAL Chi-restraints excluded: chain C residue 41 VAL Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 65 LEU Chi-restraints excluded: chain C residue 69 THR Chi-restraints excluded: chain C residue 97 GLU Chi-restraints excluded: chain C residue 111 GLU Chi-restraints excluded: chain C residue 134 THR Chi-restraints excluded: chain C residue 247 VAL Chi-restraints excluded: chain C residue 284 LEU Chi-restraints excluded: chain C residue 303 GLU Chi-restraints excluded: chain L residue 5 MET Chi-restraints excluded: chain L residue 49 ASN Chi-restraints excluded: chain L residue 139 LYS Chi-restraints excluded: chain L residue 148 TYR Chi-restraints excluded: chain L residue 204 LEU Chi-restraints excluded: chain L residue 300 LEU Chi-restraints excluded: chain L residue 304 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 88 optimal weight: 6.9990 chunk 33 optimal weight: 0.6980 chunk 73 optimal weight: 2.9990 chunk 10 optimal weight: 2.9990 chunk 38 optimal weight: 2.9990 chunk 35 optimal weight: 1.9990 chunk 9 optimal weight: 1.9990 chunk 6 optimal weight: 0.8980 chunk 68 optimal weight: 2.9990 chunk 80 optimal weight: 10.0000 chunk 101 optimal weight: 5.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3858 r_free = 0.3858 target = 0.170585 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.124333 restraints weight = 10709.474| |-----------------------------------------------------------------------------| r_work (start): 0.3298 rms_B_bonded: 1.77 r_work: 0.3079 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.3079 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7840 moved from start: 0.2493 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 10386 Z= 0.187 Angle : 0.662 7.849 14034 Z= 0.344 Chirality : 0.044 0.160 1573 Planarity : 0.005 0.102 1764 Dihedral : 6.767 71.600 1361 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.24 % Allowed : 9.50 % Favored : 90.26 % Rotamer: Outliers : 4.23 % Allowed : 17.89 % Favored : 77.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 8.57 % Twisted General : 0.16 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.64 (0.23), residues: 1242 helix: -0.15 (0.28), residues: 369 sheet: -1.81 (0.26), residues: 375 loop : -2.88 (0.25), residues: 498 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 323 HIS 0.003 0.001 HIS A 310 PHE 0.025 0.002 PHE L 485 TYR 0.018 0.002 TYR B 164 ARG 0.004 0.000 ARG B 120 Details of bonding type rmsd hydrogen bonds : bond 0.03358 ( 443) hydrogen bonds : angle 4.87037 ( 1287) covalent geometry : bond 0.00435 (10386) covalent geometry : angle 0.66203 (14034) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 1149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 127 time to evaluate : 1.210 Fit side-chains REVERT: A 157 ARG cc_start: 0.7884 (ptt90) cc_final: 0.7561 (ptt180) REVERT: A 266 MET cc_start: 0.9168 (mmt) cc_final: 0.8928 (mmm) REVERT: A 385 ASP cc_start: 0.8298 (m-30) cc_final: 0.7695 (m-30) REVERT: A 390 TYR cc_start: 0.8797 (p90) cc_final: 0.8454 (p90) REVERT: B 136 LYS cc_start: 0.8289 (mttp) cc_final: 0.7872 (mmtt) REVERT: B 189 MET cc_start: 0.9164 (mmm) cc_final: 0.8434 (mmt) REVERT: C 40 MET cc_start: 0.8921 (ptt) cc_final: 0.8706 (ptm) REVERT: C 66 ASP cc_start: 0.4683 (p0) cc_final: 0.4317 (p0) REVERT: C 102 ILE cc_start: 0.8104 (mm) cc_final: 0.7732 (mm) REVERT: C 111 GLU cc_start: 0.8239 (OUTLIER) cc_final: 0.7810 (tm-30) REVERT: C 119 ASP cc_start: 0.8021 (t0) cc_final: 0.7730 (t0) REVERT: C 303 GLU cc_start: 0.7714 (OUTLIER) cc_final: 0.7477 (pt0) REVERT: C 317 MET cc_start: 0.8103 (tpp) cc_final: 0.7835 (tpp) REVERT: L 13 TYR cc_start: 0.6418 (m-10) cc_final: 0.6024 (m-80) REVERT: L 38 ARG cc_start: 0.7391 (ttp-170) cc_final: 0.7103 (ttp-170) REVERT: L 49 ASN cc_start: 0.7397 (OUTLIER) cc_final: 0.6975 (m-40) REVERT: L 85 MET cc_start: 0.1150 (mmp) cc_final: 0.0826 (mtp) REVERT: L 146 MET cc_start: 0.8357 (ptp) cc_final: 0.8144 (ptm) REVERT: L 166 GLN cc_start: 0.8699 (OUTLIER) cc_final: 0.8275 (mt0) REVERT: L 254 TYR cc_start: 0.7472 (t80) cc_final: 0.6929 (t80) REVERT: L 304 GLU cc_start: 0.6492 (OUTLIER) cc_final: 0.6191 (pt0) REVERT: L 435 TRP cc_start: 0.7162 (OUTLIER) cc_final: 0.5626 (t60) outliers start: 48 outliers final: 33 residues processed: 158 average time/residue: 0.2319 time to fit residues: 51.1306 Evaluate side-chains 156 residues out of total 1149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 117 time to evaluate : 1.058 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 197 TRP Chi-restraints excluded: chain A residue 203 LEU Chi-restraints excluded: chain A residue 213 SER Chi-restraints excluded: chain A residue 248 SER Chi-restraints excluded: chain A residue 332 SER Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 359 SER Chi-restraints excluded: chain A residue 396 SER Chi-restraints excluded: chain A residue 420 VAL Chi-restraints excluded: chain A residue 440 THR Chi-restraints excluded: chain A residue 481 LEU Chi-restraints excluded: chain B residue 22 THR Chi-restraints excluded: chain B residue 43 THR Chi-restraints excluded: chain B residue 45 THR Chi-restraints excluded: chain B residue 110 THR Chi-restraints excluded: chain B residue 120 ARG Chi-restraints excluded: chain B residue 123 ASN Chi-restraints excluded: chain B residue 139 ILE Chi-restraints excluded: chain B residue 144 VAL Chi-restraints excluded: chain B residue 203 THR Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 252 VAL Chi-restraints excluded: chain C residue 41 VAL Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 69 THR Chi-restraints excluded: chain C residue 97 GLU Chi-restraints excluded: chain C residue 111 GLU Chi-restraints excluded: chain C residue 134 THR Chi-restraints excluded: chain C residue 247 VAL Chi-restraints excluded: chain C residue 284 LEU Chi-restraints excluded: chain C residue 303 GLU Chi-restraints excluded: chain L residue 5 MET Chi-restraints excluded: chain L residue 49 ASN Chi-restraints excluded: chain L residue 148 TYR Chi-restraints excluded: chain L residue 166 GLN Chi-restraints excluded: chain L residue 204 LEU Chi-restraints excluded: chain L residue 241 LEU Chi-restraints excluded: chain L residue 304 GLU Chi-restraints excluded: chain L residue 435 TRP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 42 optimal weight: 3.9990 chunk 64 optimal weight: 0.8980 chunk 98 optimal weight: 5.9990 chunk 63 optimal weight: 2.9990 chunk 92 optimal weight: 9.9990 chunk 7 optimal weight: 0.5980 chunk 114 optimal weight: 0.0060 chunk 53 optimal weight: 0.9990 chunk 21 optimal weight: 3.9990 chunk 81 optimal weight: 10.0000 chunk 10 optimal weight: 2.9990 overall best weight: 1.1000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 421 ASN ** A 422 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 318 GLN C 258 ASN L 195 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3878 r_free = 0.3878 target = 0.172614 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.125846 restraints weight = 10731.296| |-----------------------------------------------------------------------------| r_work (start): 0.3297 rms_B_bonded: 1.92 r_work: 0.3103 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.3103 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7785 moved from start: 0.2652 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 10386 Z= 0.140 Angle : 0.630 9.259 14034 Z= 0.325 Chirality : 0.043 0.252 1573 Planarity : 0.005 0.098 1764 Dihedral : 6.530 72.781 1361 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 7.45 Ramachandran Plot: Outliers : 0.24 % Allowed : 8.86 % Favored : 90.90 % Rotamer: Outliers : 3.52 % Allowed : 18.15 % Favored : 78.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 8.57 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.46 (0.24), residues: 1242 helix: 0.05 (0.28), residues: 376 sheet: -1.61 (0.27), residues: 377 loop : -2.97 (0.25), residues: 489 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 323 HIS 0.003 0.001 HIS A 310 PHE 0.025 0.001 PHE L 485 TYR 0.015 0.001 TYR C 260 ARG 0.003 0.000 ARG B 120 Details of bonding type rmsd hydrogen bonds : bond 0.03054 ( 443) hydrogen bonds : angle 4.70799 ( 1287) covalent geometry : bond 0.00320 (10386) covalent geometry : angle 0.63002 (14034) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 1149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 130 time to evaluate : 1.245 Fit side-chains REVERT: A 157 ARG cc_start: 0.7900 (ptt90) cc_final: 0.7577 (ptt180) REVERT: A 266 MET cc_start: 0.9177 (mmt) cc_final: 0.8932 (mmm) REVERT: A 324 MET cc_start: 0.7422 (mmm) cc_final: 0.6856 (mmm) REVERT: A 385 ASP cc_start: 0.8267 (m-30) cc_final: 0.7657 (m-30) REVERT: A 390 TYR cc_start: 0.8735 (p90) cc_final: 0.8419 (p90) REVERT: B 136 LYS cc_start: 0.8266 (mttp) cc_final: 0.7852 (mmtt) REVERT: B 189 MET cc_start: 0.9133 (mmm) cc_final: 0.8323 (mmt) REVERT: C 40 MET cc_start: 0.8918 (ptt) cc_final: 0.8713 (ptm) REVERT: C 66 ASP cc_start: 0.4741 (p0) cc_final: 0.4387 (p0) REVERT: C 102 ILE cc_start: 0.8028 (mm) cc_final: 0.7781 (mm) REVERT: C 111 GLU cc_start: 0.8233 (OUTLIER) cc_final: 0.7872 (tm-30) REVERT: C 119 ASP cc_start: 0.7983 (t0) cc_final: 0.7691 (t0) REVERT: C 303 GLU cc_start: 0.7660 (OUTLIER) cc_final: 0.7436 (pt0) REVERT: C 317 MET cc_start: 0.8079 (tpp) cc_final: 0.7829 (tpp) REVERT: L 13 TYR cc_start: 0.6284 (m-10) cc_final: 0.5855 (m-80) REVERT: L 49 ASN cc_start: 0.7274 (OUTLIER) cc_final: 0.6835 (m-40) REVERT: L 85 MET cc_start: 0.1024 (mmp) cc_final: 0.0796 (mtp) REVERT: L 146 MET cc_start: 0.8360 (ptp) cc_final: 0.8159 (ptm) REVERT: L 231 LEU cc_start: 0.8178 (tt) cc_final: 0.7694 (pp) REVERT: L 254 TYR cc_start: 0.7513 (t80) cc_final: 0.6985 (t80) REVERT: L 435 TRP cc_start: 0.7047 (OUTLIER) cc_final: 0.5493 (t60) outliers start: 40 outliers final: 31 residues processed: 154 average time/residue: 0.2836 time to fit residues: 62.5289 Evaluate side-chains 154 residues out of total 1149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 119 time to evaluate : 1.172 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 179 SER Chi-restraints excluded: chain A residue 197 TRP Chi-restraints excluded: chain A residue 203 LEU Chi-restraints excluded: chain A residue 213 SER Chi-restraints excluded: chain A residue 248 SER Chi-restraints excluded: chain A residue 332 SER Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 359 SER Chi-restraints excluded: chain A residue 481 LEU Chi-restraints excluded: chain B residue 22 THR Chi-restraints excluded: chain B residue 43 THR Chi-restraints excluded: chain B residue 45 THR Chi-restraints excluded: chain B residue 110 THR Chi-restraints excluded: chain B residue 120 ARG Chi-restraints excluded: chain B residue 123 ASN Chi-restraints excluded: chain B residue 139 ILE Chi-restraints excluded: chain B residue 203 THR Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 252 VAL Chi-restraints excluded: chain B residue 291 SER Chi-restraints excluded: chain C residue 41 VAL Chi-restraints excluded: chain C residue 69 THR Chi-restraints excluded: chain C residue 97 GLU Chi-restraints excluded: chain C residue 111 GLU Chi-restraints excluded: chain C residue 134 THR Chi-restraints excluded: chain C residue 247 VAL Chi-restraints excluded: chain C residue 284 LEU Chi-restraints excluded: chain C residue 303 GLU Chi-restraints excluded: chain L residue 5 MET Chi-restraints excluded: chain L residue 49 ASN Chi-restraints excluded: chain L residue 148 TYR Chi-restraints excluded: chain L residue 204 LEU Chi-restraints excluded: chain L residue 300 LEU Chi-restraints excluded: chain L residue 411 ILE Chi-restraints excluded: chain L residue 435 TRP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 23 optimal weight: 3.9990 chunk 111 optimal weight: 20.0000 chunk 29 optimal weight: 1.9990 chunk 17 optimal weight: 1.9990 chunk 14 optimal weight: 4.9990 chunk 95 optimal weight: 9.9990 chunk 41 optimal weight: 4.9990 chunk 11 optimal weight: 2.9990 chunk 55 optimal weight: 9.9990 chunk 98 optimal weight: 4.9990 chunk 121 optimal weight: 7.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 133 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.167954 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 88)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.118324 restraints weight = 10816.797| |-----------------------------------------------------------------------------| r_work (start): 0.3210 rms_B_bonded: 1.80 r_work: 0.3036 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.3036 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7878 moved from start: 0.2559 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.054 10386 Z= 0.307 Angle : 0.777 12.954 14034 Z= 0.398 Chirality : 0.049 0.232 1573 Planarity : 0.006 0.112 1764 Dihedral : 7.073 70.937 1361 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 8.54 Ramachandran Plot: Outliers : 0.32 % Allowed : 10.63 % Favored : 89.05 % Rotamer: Outliers : 4.32 % Allowed : 18.50 % Favored : 77.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 8.57 % Twisted General : 0.16 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.66 (0.23), residues: 1242 helix: -0.13 (0.28), residues: 362 sheet: -1.84 (0.26), residues: 393 loop : -2.88 (0.25), residues: 487 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP L 435 HIS 0.005 0.001 HIS A 169 PHE 0.040 0.003 PHE L 298 TYR 0.022 0.002 TYR A 140 ARG 0.007 0.001 ARG A 211 Details of bonding type rmsd hydrogen bonds : bond 0.03885 ( 443) hydrogen bonds : angle 5.01344 ( 1287) covalent geometry : bond 0.00727 (10386) covalent geometry : angle 0.77738 (14034) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 1149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 115 time to evaluate : 3.158 Fit side-chains REVERT: A 157 ARG cc_start: 0.7867 (ptt90) cc_final: 0.7518 (ptt-90) REVERT: A 385 ASP cc_start: 0.8331 (m-30) cc_final: 0.7806 (m-30) REVERT: A 390 TYR cc_start: 0.8886 (p90) cc_final: 0.8487 (p90) REVERT: B 136 LYS cc_start: 0.8324 (mttp) cc_final: 0.7939 (mmtt) REVERT: B 189 MET cc_start: 0.9152 (mmm) cc_final: 0.8439 (mmt) REVERT: C 40 MET cc_start: 0.8960 (ptt) cc_final: 0.8744 (ptm) REVERT: C 102 ILE cc_start: 0.8103 (mm) cc_final: 0.7821 (mm) REVERT: C 111 GLU cc_start: 0.8327 (OUTLIER) cc_final: 0.7779 (tm-30) REVERT: C 119 ASP cc_start: 0.8062 (t0) cc_final: 0.7785 (t0) REVERT: C 303 GLU cc_start: 0.7682 (OUTLIER) cc_final: 0.7416 (pt0) REVERT: L 49 ASN cc_start: 0.7351 (OUTLIER) cc_final: 0.6868 (m-40) REVERT: L 85 MET cc_start: 0.1411 (mmp) cc_final: 0.1033 (mtp) REVERT: L 146 MET cc_start: 0.8226 (ptp) cc_final: 0.7963 (ptm) REVERT: L 166 GLN cc_start: 0.8734 (OUTLIER) cc_final: 0.8405 (mt0) REVERT: L 168 MET cc_start: 0.7813 (mtp) cc_final: 0.7577 (mtp) REVERT: L 254 TYR cc_start: 0.7611 (t80) cc_final: 0.7003 (t80) REVERT: L 435 TRP cc_start: 0.7338 (OUTLIER) cc_final: 0.7040 (t60) outliers start: 49 outliers final: 36 residues processed: 152 average time/residue: 0.4350 time to fit residues: 96.4851 Evaluate side-chains 152 residues out of total 1149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 111 time to evaluate : 2.240 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 179 SER Chi-restraints excluded: chain A residue 197 TRP Chi-restraints excluded: chain A residue 203 LEU Chi-restraints excluded: chain A residue 213 SER Chi-restraints excluded: chain A residue 248 SER Chi-restraints excluded: chain A residue 253 SER Chi-restraints excluded: chain A residue 327 ASP Chi-restraints excluded: chain A residue 332 SER Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 359 SER Chi-restraints excluded: chain A residue 396 SER Chi-restraints excluded: chain A residue 420 VAL Chi-restraints excluded: chain A residue 427 LEU Chi-restraints excluded: chain A residue 440 THR Chi-restraints excluded: chain A residue 481 LEU Chi-restraints excluded: chain B residue 22 THR Chi-restraints excluded: chain B residue 43 THR Chi-restraints excluded: chain B residue 45 THR Chi-restraints excluded: chain B residue 110 THR Chi-restraints excluded: chain B residue 120 ARG Chi-restraints excluded: chain B residue 123 ASN Chi-restraints excluded: chain B residue 139 ILE Chi-restraints excluded: chain B residue 144 VAL Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 252 VAL Chi-restraints excluded: chain B residue 291 SER Chi-restraints excluded: chain C residue 41 VAL Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 69 THR Chi-restraints excluded: chain C residue 97 GLU Chi-restraints excluded: chain C residue 111 GLU Chi-restraints excluded: chain C residue 134 THR Chi-restraints excluded: chain C residue 247 VAL Chi-restraints excluded: chain C residue 284 LEU Chi-restraints excluded: chain C residue 303 GLU Chi-restraints excluded: chain L residue 5 MET Chi-restraints excluded: chain L residue 49 ASN Chi-restraints excluded: chain L residue 148 TYR Chi-restraints excluded: chain L residue 166 GLN Chi-restraints excluded: chain L residue 204 LEU Chi-restraints excluded: chain L residue 435 TRP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 39 optimal weight: 0.7980 chunk 63 optimal weight: 1.9990 chunk 27 optimal weight: 1.9990 chunk 35 optimal weight: 0.0670 chunk 115 optimal weight: 20.0000 chunk 15 optimal weight: 1.9990 chunk 52 optimal weight: 0.8980 chunk 116 optimal weight: 8.9990 chunk 76 optimal weight: 3.9990 chunk 61 optimal weight: 2.9990 chunk 89 optimal weight: 7.9990 overall best weight: 1.1522 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3881 r_free = 0.3881 target = 0.172796 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 88)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.124529 restraints weight = 10681.772| |-----------------------------------------------------------------------------| r_work (start): 0.3270 rms_B_bonded: 1.81 r_work: 0.3104 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.2953 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.2953 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7922 moved from start: 0.2738 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 10386 Z= 0.148 Angle : 0.665 14.660 14034 Z= 0.338 Chirality : 0.043 0.217 1573 Planarity : 0.005 0.102 1764 Dihedral : 6.671 73.059 1361 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 7.85 Ramachandran Plot: Outliers : 0.24 % Allowed : 8.45 % Favored : 91.30 % Rotamer: Outliers : 3.96 % Allowed : 19.21 % Favored : 76.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 8.57 % Twisted General : 0.16 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.45 (0.24), residues: 1242 helix: 0.06 (0.28), residues: 377 sheet: -1.62 (0.27), residues: 382 loop : -2.96 (0.25), residues: 483 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 301 HIS 0.004 0.001 HIS A 310 PHE 0.030 0.002 PHE L 292 TYR 0.015 0.001 TYR C 260 ARG 0.004 0.000 ARG A 211 Details of bonding type rmsd hydrogen bonds : bond 0.03146 ( 443) hydrogen bonds : angle 4.74978 ( 1287) covalent geometry : bond 0.00339 (10386) covalent geometry : angle 0.66475 (14034) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 1149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 120 time to evaluate : 1.221 Fit side-chains REVERT: A 157 ARG cc_start: 0.8074 (ptt90) cc_final: 0.7716 (ptt180) REVERT: A 266 MET cc_start: 0.9307 (mmt) cc_final: 0.9028 (mmm) REVERT: A 385 ASP cc_start: 0.8429 (m-30) cc_final: 0.7885 (m-30) REVERT: A 390 TYR cc_start: 0.8818 (p90) cc_final: 0.8483 (p90) REVERT: B 136 LYS cc_start: 0.8283 (mttp) cc_final: 0.7814 (mmtt) REVERT: B 189 MET cc_start: 0.9204 (mmm) cc_final: 0.8537 (mmt) REVERT: B 249 HIS cc_start: 0.7849 (OUTLIER) cc_final: 0.7409 (t70) REVERT: C 102 ILE cc_start: 0.7999 (mm) cc_final: 0.7734 (mm) REVERT: C 111 GLU cc_start: 0.8322 (OUTLIER) cc_final: 0.7972 (tm-30) REVERT: C 119 ASP cc_start: 0.8289 (t0) cc_final: 0.8026 (t0) REVERT: C 303 GLU cc_start: 0.7890 (OUTLIER) cc_final: 0.7653 (pt0) REVERT: L 49 ASN cc_start: 0.7563 (OUTLIER) cc_final: 0.7136 (m-40) REVERT: L 85 MET cc_start: 0.1420 (mmp) cc_final: 0.0986 (mtp) REVERT: L 146 MET cc_start: 0.8380 (ptp) cc_final: 0.8168 (ptm) REVERT: L 166 GLN cc_start: 0.8848 (OUTLIER) cc_final: 0.8483 (mt0) REVERT: L 168 MET cc_start: 0.8076 (mtp) cc_final: 0.7865 (mtp) REVERT: L 231 LEU cc_start: 0.8209 (tt) cc_final: 0.7641 (pp) REVERT: L 254 TYR cc_start: 0.7625 (t80) cc_final: 0.6933 (t80) REVERT: L 292 PHE cc_start: 0.6612 (t80) cc_final: 0.6401 (t80) REVERT: L 435 TRP cc_start: 0.7265 (OUTLIER) cc_final: 0.7002 (t60) outliers start: 45 outliers final: 33 residues processed: 147 average time/residue: 0.2272 time to fit residues: 47.4044 Evaluate side-chains 158 residues out of total 1149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 119 time to evaluate : 1.060 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 179 SER Chi-restraints excluded: chain A residue 197 TRP Chi-restraints excluded: chain A residue 203 LEU Chi-restraints excluded: chain A residue 213 SER Chi-restraints excluded: chain A residue 248 SER Chi-restraints excluded: chain A residue 253 SER Chi-restraints excluded: chain A residue 332 SER Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 359 SER Chi-restraints excluded: chain A residue 396 SER Chi-restraints excluded: chain A residue 420 VAL Chi-restraints excluded: chain A residue 440 THR Chi-restraints excluded: chain A residue 481 LEU Chi-restraints excluded: chain B residue 22 THR Chi-restraints excluded: chain B residue 43 THR Chi-restraints excluded: chain B residue 45 THR Chi-restraints excluded: chain B residue 110 THR Chi-restraints excluded: chain B residue 120 ARG Chi-restraints excluded: chain B residue 123 ASN Chi-restraints excluded: chain B residue 139 ILE Chi-restraints excluded: chain B residue 144 VAL Chi-restraints excluded: chain B residue 203 THR Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 249 HIS Chi-restraints excluded: chain B residue 252 VAL Chi-restraints excluded: chain B residue 291 SER Chi-restraints excluded: chain C residue 41 VAL Chi-restraints excluded: chain C residue 69 THR Chi-restraints excluded: chain C residue 111 GLU Chi-restraints excluded: chain C residue 134 THR Chi-restraints excluded: chain C residue 247 VAL Chi-restraints excluded: chain C residue 284 LEU Chi-restraints excluded: chain C residue 303 GLU Chi-restraints excluded: chain L residue 5 MET Chi-restraints excluded: chain L residue 49 ASN Chi-restraints excluded: chain L residue 148 TYR Chi-restraints excluded: chain L residue 166 GLN Chi-restraints excluded: chain L residue 204 LEU Chi-restraints excluded: chain L residue 435 TRP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 13 optimal weight: 0.6980 chunk 62 optimal weight: 0.4980 chunk 42 optimal weight: 3.9990 chunk 27 optimal weight: 2.9990 chunk 99 optimal weight: 6.9990 chunk 59 optimal weight: 0.9980 chunk 8 optimal weight: 4.9990 chunk 18 optimal weight: 6.9990 chunk 53 optimal weight: 0.6980 chunk 6 optimal weight: 2.9990 chunk 50 optimal weight: 0.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 200 ASN ** A 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 49 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3912 r_free = 0.3912 target = 0.174935 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.145034 restraints weight = 10807.923| |-----------------------------------------------------------------------------| r_work (start): 0.3604 rms_B_bonded: 1.15 r_work: 0.3300 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work (final): 0.3300 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7838 moved from start: 0.2962 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 10386 Z= 0.121 Angle : 0.632 14.136 14034 Z= 0.320 Chirality : 0.042 0.215 1573 Planarity : 0.005 0.100 1764 Dihedral : 5.904 53.861 1358 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.24 % Allowed : 8.37 % Favored : 91.38 % Rotamer: Outliers : 3.08 % Allowed : 19.91 % Favored : 77.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 8.57 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.16 (0.24), residues: 1242 helix: 0.37 (0.28), residues: 381 sheet: -1.43 (0.27), residues: 389 loop : -2.91 (0.25), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 301 HIS 0.003 0.001 HIS A 310 PHE 0.028 0.001 PHE L 292 TYR 0.015 0.001 TYR C 260 ARG 0.003 0.000 ARG A 211 Details of bonding type rmsd hydrogen bonds : bond 0.02847 ( 443) hydrogen bonds : angle 4.54876 ( 1287) covalent geometry : bond 0.00274 (10386) covalent geometry : angle 0.63154 (14034) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 1149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 131 time to evaluate : 1.076 Fit side-chains REVERT: A 266 MET cc_start: 0.9066 (mmt) cc_final: 0.8809 (mmm) REVERT: A 324 MET cc_start: 0.7484 (mmm) cc_final: 0.6983 (mmm) REVERT: A 385 ASP cc_start: 0.8029 (m-30) cc_final: 0.7565 (m-30) REVERT: A 390 TYR cc_start: 0.8414 (p90) cc_final: 0.8213 (p90) REVERT: A 455 PHE cc_start: 0.8504 (m-80) cc_final: 0.8287 (m-80) REVERT: B 136 LYS cc_start: 0.8152 (mttp) cc_final: 0.7936 (mmtt) REVERT: B 178 GLN cc_start: 0.8732 (mt0) cc_final: 0.8505 (tt0) REVERT: B 189 MET cc_start: 0.9048 (mmm) cc_final: 0.8178 (mmt) REVERT: B 249 HIS cc_start: 0.7761 (OUTLIER) cc_final: 0.7373 (t70) REVERT: C 66 ASP cc_start: 0.4956 (p0) cc_final: 0.4551 (p0) REVERT: C 102 ILE cc_start: 0.8247 (mm) cc_final: 0.8037 (mm) REVERT: C 111 GLU cc_start: 0.8179 (OUTLIER) cc_final: 0.7938 (tm-30) REVERT: C 119 ASP cc_start: 0.8029 (t0) cc_final: 0.7726 (t0) REVERT: C 318 SER cc_start: 0.8212 (t) cc_final: 0.8005 (t) REVERT: L 13 TYR cc_start: 0.6462 (m-10) cc_final: 0.5979 (m-80) REVERT: L 166 GLN cc_start: 0.8503 (OUTLIER) cc_final: 0.8217 (tt0) REVERT: L 231 LEU cc_start: 0.8222 (tt) cc_final: 0.7821 (pp) REVERT: L 254 TYR cc_start: 0.7375 (t80) cc_final: 0.6980 (t80) REVERT: L 435 TRP cc_start: 0.7054 (OUTLIER) cc_final: 0.5818 (t60) outliers start: 35 outliers final: 28 residues processed: 151 average time/residue: 0.2209 time to fit residues: 47.0100 Evaluate side-chains 156 residues out of total 1149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 124 time to evaluate : 1.104 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 179 SER Chi-restraints excluded: chain A residue 197 TRP Chi-restraints excluded: chain A residue 203 LEU Chi-restraints excluded: chain A residue 213 SER Chi-restraints excluded: chain A residue 248 SER Chi-restraints excluded: chain A residue 332 SER Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 359 SER Chi-restraints excluded: chain A residue 396 SER Chi-restraints excluded: chain A residue 420 VAL Chi-restraints excluded: chain A residue 440 THR Chi-restraints excluded: chain A residue 481 LEU Chi-restraints excluded: chain B residue 43 THR Chi-restraints excluded: chain B residue 45 THR Chi-restraints excluded: chain B residue 120 ARG Chi-restraints excluded: chain B residue 123 ASN Chi-restraints excluded: chain B residue 139 ILE Chi-restraints excluded: chain B residue 144 VAL Chi-restraints excluded: chain B residue 203 THR Chi-restraints excluded: chain B residue 249 HIS Chi-restraints excluded: chain B residue 252 VAL Chi-restraints excluded: chain B residue 291 SER Chi-restraints excluded: chain C residue 65 LEU Chi-restraints excluded: chain C residue 69 THR Chi-restraints excluded: chain C residue 111 GLU Chi-restraints excluded: chain C residue 247 VAL Chi-restraints excluded: chain C residue 284 LEU Chi-restraints excluded: chain L residue 49 ASN Chi-restraints excluded: chain L residue 148 TYR Chi-restraints excluded: chain L residue 166 GLN Chi-restraints excluded: chain L residue 204 LEU Chi-restraints excluded: chain L residue 435 TRP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 115 optimal weight: 20.0000 chunk 75 optimal weight: 0.0370 chunk 108 optimal weight: 8.9990 chunk 25 optimal weight: 0.9990 chunk 110 optimal weight: 0.9990 chunk 34 optimal weight: 6.9990 chunk 48 optimal weight: 3.9990 chunk 69 optimal weight: 0.5980 chunk 65 optimal weight: 3.9990 chunk 97 optimal weight: 5.9990 chunk 42 optimal weight: 1.9990 overall best weight: 0.9264 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 49 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3911 r_free = 0.3911 target = 0.174842 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.143958 restraints weight = 10729.016| |-----------------------------------------------------------------------------| r_work (start): 0.3542 rms_B_bonded: 1.14 r_work: 0.3237 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3070 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.3070 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7974 moved from start: 0.3028 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 10386 Z= 0.130 Angle : 0.640 14.080 14034 Z= 0.324 Chirality : 0.042 0.207 1573 Planarity : 0.005 0.101 1764 Dihedral : 5.876 54.391 1358 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 7.75 Ramachandran Plot: Outliers : 0.24 % Allowed : 8.62 % Favored : 91.14 % Rotamer: Outliers : 3.08 % Allowed : 19.91 % Favored : 77.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 8.57 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.97 (0.24), residues: 1242 helix: 0.53 (0.28), residues: 381 sheet: -1.30 (0.27), residues: 387 loop : -2.83 (0.25), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 301 HIS 0.003 0.001 HIS A 310 PHE 0.027 0.001 PHE L 292 TYR 0.017 0.001 TYR C 140 ARG 0.004 0.000 ARG A 211 Details of bonding type rmsd hydrogen bonds : bond 0.02938 ( 443) hydrogen bonds : angle 4.53942 ( 1287) covalent geometry : bond 0.00295 (10386) covalent geometry : angle 0.63979 (14034) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5488.78 seconds wall clock time: 97 minutes 24.59 seconds (5844.59 seconds total)